Currently, a large majority of HLA genotyping tools employ some form of matching individual sequence reads to the reference allele sequences followed by some scoring strategy to account for mapping uncertainty and signal noise. In this chapter we first briefly review the source of this data. For example, virtually all of the advances in the analysis of genetic diseases require new computer-enabled technologies. Abstract. Reference Manager
For example, the high-stakes economic game of biotechnology pits two groups against each other. They each provide searching and browsing tools for the sequence of the Arabidopsis genome as well as annotation of the genome analyzed by the individual groups' suite of programs. This becomes especially important if indels in a sample identify a true variant not yet described in the HLA reference database used for graph construction.As discussed in the section Sequencing Platforms, indels can be common artefacts introduced during sequencing. Thus, for any given short read, there are potentially many equally good matches and most off-the-shelf mappers are optimised for speed and not for exhaustively reporting all possible matches. We found an already existing MyKarger account with this e-mail address:
This may be explained by the fact that many of these tools have been designed in the context of cancer immunotherapy with the express goal to predict HLA class I and class II binding neoepitopes. Among sample preparation methods used for HLA typing we can distinguish between HLA-targeted approaches (e.g., PCR-based target amplification, hybridisation-based capture techniques) and HLA-untargeted approaches (e.g., whole-genome sequencing [WGS], whole-exome sequencing [WES], transcriptome sequencing).The most commonly used technique for target enrichment for HLA genotyping is PCR (Fig. Fundamentally, NGS platforms may be classified based on the read lengths they are capable of generating. Another challenge for typing is the determination of homozygosity versus heterozygosity at a locus. DNA vaccines promise cures for not only genetic diseases, but also for acquired diseases such as AIDS. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.The exceptionally polymorphic human leukocyte antigen (HLA) system contains numerous genes that encode key components of the human adaptive immune system [Currently, more than 21,000 named alleles are reported in the central public reference sequence repository for HLA allele variation for these 6 genes alone (IPD-IMGT/HLA release 3.36.0 [The hallmark of the various NGS technologies is massively parallel sequencing of single DNA molecules (clonal sequencing) [Concomitantly, NGS has injected a heavy dose of bioinformatics into the field of HLA genotyping. This development eliminated several challenges posed by microarray technologies, including the limited dynamic range of detection 5. Continuing Education. In our experience, once polymorphisms are separated by a long homozygous stretch of more than about 1 kb, resolution of phase between the two chromosomes tends to fail using short-read technologies as read pairs no longer reliably span this distance.
Ideally, a genotyping algorithm would also be able to report differences to known alleles and provide a sequence which can be submitted to the IPD to be included in the database. The key challenges to bioinformatics essentially all relate to the current flood of raw data, aggregate information, and evolving knowledge arising from the study of the genome and its manifestation. “Gene Ontology: Tool for the Unification of Biology,” Herrgard, M. and Palsson, B.
NGS reads are clonal in nature and adequate algorithms can be used, in principle, to sort even short reads of less than 100 bp into fully phased haplotypes.
The amounts of data generated by NGS platforms are typically magnitudes larger compared to Sanger sequencing. State of the Art. Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping.